The overarching goal of this proposal is to identify key methylation marks that regulate expression of mRNAs and miRNAs involved in pathogenesis of idiopathic pulmonary fibrosis (IPF). IPF is an untreatable and often fatal lung disease that is increasing in prevalence and is likely the result of complex interactions between genetic and environmental factors such as cigarette smoke. Although it is currently believed that the injury to the alveolar epithelium initiates a cascade of events that lead to accumulation of extracellular matrix, dysregulated wound repair, and lung remodeling, dramatic changes in mRNA and miRNA expression changes and cellular phenotypes in IPF lung suggest that many different molecular processes are involved. Several lines of evidence support the role of epigenetic regulation of gene expression in IPF lung. Firstly, recent studies have demonstrated that cigarette smoke, a key environmental risk factor for IPF, has an influence on the epigenome and on methylation of specific promoters in genes involved in pathogenesis of IPF. Secondly, IPF is a genetic disease, and genetic factors influence DNA methylation. Thirdly, focused studies to date have demonstrated the influence of epigenetic marks on expression of key genes in IPF. Fourthly, data are emerging on the role of DNA methylation in regulation of miRNA expression in IPF. Finally, our recent work demonstrates extensive methylation changes on the genomic scale in IPF lung. The hypothesis of this proposal is that DNA methylation marks regulate expression of key fibrotic mRNAs and miRNAs in the IPF lung. We will test this hypothesis using existing Lung Genomics Research Consortium (LGRC), ENCyclopedia Of DNA Elements (ENCODE) and Roadmap Epigenomics (RE) project data. We will first perform methyl-expression quantitative trait locus (me-eQTL) mapping to identify differentially methylated regions (DMRs) that control mRNAs and miRNA expression as well as mRNA alternative splicing in cis and trans in IPF lung tissue. We will then prioritize the DMRs based on their regulatory potential in the lung using available ENCODE and RE methylation, histone mark, transcription factor binding, and chromatin accessibility data in lung tissue, relevant primary cells and cell lines. Results of this work will be used as preliminary data for a R01 application that will explore the influence of cigarette smoke and genetic variants on identified methylation marks and will perform functional studies to determine how treatment with agents that alter methylation marks influence expression of target mRNAs and miRNAs as well as fibro-proliferative phenotypes in vitro and in vivo.